When Mayor Bill de Blasio took office, it seemed like the start of a bright new day in the relationship between City Hall and the people who run New York City’s schools.

Rather than close struggling schools, as his predecessor Michael R. Bloomberg had done, Mr. de Blasio promised to support them. In November 2014, he and his schools chancellor, Carmen Fariña, announced a program to funnel resources, training and social services into 94 of the lowest-performing schools.

At the time, Ernest A. Logan, the president of the union that represents the city’s principals and assistant principals, lauded Mr. de Blasio, saying that the initiative demonstrated a “philosophy of collaboration over competition” and reflected “the deeply held values of most of our school leaders.”

Now, however, Mr. Logan says he — and by extension, the 6,000 members of the Council of School Supervisors and Administrators — has lost confidence in the de Blasio administration. In a column to be published in the union’s newsletter this month, Mr. Logan writes of the Education Department, “Sadly, in the timeworn tradition of the D.O.E., there are so many cooks running around in the kitchen, the chefs don’t know what kind of dish they’re concocting.” So many different mandates have been thrown at these schools, he writes, that “all we have is a recipe for disaster.”

In an interview last week, Mr. Logan said of the school-turnaround effort, “This became a political mess, because the mayor made this his political thing.”

He added, “They’ve lost their focus on kids.”

Mr. Logan said principals in the 94 schools were being overwhelmed with paperwork and meetings and micromanaged to the point that they could not do what they thought was best for their schools. He said he believed the mayor’s approach was destined to fail if the city did not change its strategy.

While it does not have the political clout of the city’s teachers’ union, the United Federation of Teachers, with its nearly 200,000 members and millions of dollars to spend on lobbying and political contributions, the administrators’ union is a critical ally in any effort to transform the city’s schools. Losing its support would make the task more difficult.

Few principals were willing to comment publicly on their relationship with the Education Department, fearing repercussions. But Santiago Taveras, the principal of DeWitt Clinton High School in the Bronx, one of the schools in the turnaround program, said one of the biggest issues was the department’s pulling teachers and administrators out of school for meetings and training.

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Santiago Taveras, the principal of DeWitt Clinton High School in the Bronx, a school in the mayor’s turnaround program.CreditNicole Bengiveno/The New York Times

Mr. Taveras was a deputy chancellor in the Bloomberg administration and oversaw many school closings. In 2013 he became a principal again with the aim of reinvigorating Clinton, whose enrollment has dwindled in recent years to about 1,700 students from 4,000. Mr. Taveras is being investigated for accusations that he changed students’ grades to improve the school’s outcomes, which he has denied.

Mr. Taveras says five of his teachers and one assistant principal are required to attend a full day of training every other week in a writing program that is being implemented in the high schools.

Making things worse, he said, is that the program, while good, was announced on Sept. 3, six days before the start of the school year, leaving almost no time to prepare or to train teachers.

Another high school principal, who spoke on the condition of anonymity to avoid becoming a target of either the Education Department or the teachers’ union, was more blunt. Not only did he feel inundated by meetings and paperwork, he said, he was frequently overruled by the bureaucrats overseeing the turnaround effort.

“I feel like I can’t actually get anything done, because I have to go through this chain, and if the chain decides that that’s not what they want,” he cannot proceed, the principal said. “It’s completely annoying to be constantly second-guessed.”

He added, “There’s so many things that everybody is asking you to do that half the time you can’t even read your emails, let alone actually go into a classroom.”

In an interview, Ms. Fariña defended the administration’s approach and said the work of improving schools was urgent and was “not about how we make certain people happy — it’s about how we get outcomes in our kids.”

Wiley Norvell, a spokesman for Mr. de Blasio, said: “When you change the status quo, you’re going to have critics along the way. These schools are getting the new leadership and support they need to succeed.”

Efforts to transform schools are contentious, of course, and school leaders who are deemed to be failing are not likely to be pleased. Some principals in the turnaround program said they were excited about the resources and support they were getting.

“This has been a windfall for my school,” said Brian Bradley, the principal of Renaissance School of the Arts, a middle school in East Harlem. He is now able to offer programs until 6 p.m. for all of his students, he said. And while before his students had arts classes only twice a week, now they were getting them every day. He said he also valued the guidance he was receiving from his superintendent’s office.

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Carmen Fariña, the city’s schools chancellor, defended the administration’s actions.CreditHilary Swift for The New York Times

As to principals’ feeling micromanaged, Ms. Fariña said that oversight was necessary, and that she believed autonomy was something principals had to earn.

Referring to having replaced roughly a third of the principals in these schools, she said, “We didn’t put in one-third new principals to continue to do the same old, same old.”

Mr. Logan, for his part, said the fact that Ms. Fariña had been able to choose the principals she wanted made the interference particularly galling.

“If you have selected these people to run your schools, then let them run it,” he said.

He had other concerns, as well. He said the 94 schools were being subjected to numerous, redundant assessments, by different authorities and according to different standards, all of which consumed principals’ time. One assessment, for instance, involves three days of visits and data gathering and has to be conducted three times a year, meaning that it eats up nine days.

Retired principals assigned to coach principals of struggling schools, who the union believed were to be confidential advisers, have instead been instructed to report back to the principals’ supervisors, Mr. Logan said. He said he would be sending a notice to his members warning them that the coaches “are not people who are necessarily there to support you.”

An even more serious problem, he said, is the number of principals across the system who are under some kind of investigation. The number of complaints received by the special commissioner of investigation for the school system, Richard J. Condon, is at a record high, with 5,566 in 2015.

Mr. Logan said 1,400 of the union’s members currently had an open investigation, and that he and his members felt many of them were dubious, touched off by disgruntled staff members.

He said principals at the schools in the turnaround program were particularly at risk, because they were aggressively trying to make changes in their schools, pushing teachers hard and in some cases giving them negative evaluations.

During the Bloomberg administration, Mr. Logan was a frequent critic of the Education Department, including of the policy of closing schools. In the interview this week, he said many of his members had initially been pleased by the appointment of Ms. Fariña, a former teacher and principal, who as chancellor spoke about respecting educators.

Nonetheless, he said, if he were to ask all of his members now, “I think a majority of them would say they probably had a better shot of being able to effectively do their job under the old administration.”